Conservation analysis of class‐specific positions in cytochrome P450 monooxygenases: Functional and structural relevance

Cytochrome P450 monooxygenases (CYPs) constitute a ubiquitous, highly divergent protein family. Nevertheless, all CYPs share a common fold and conserved catalytic machinery. Based on the electron donor system, 10 classes of CYPs have been described, but most CYPs are members of class I accepting electrons from ferredoxin which is being reduced by FAD‐containing reductase, or class II accepting electrons from FAD‐ and FMN‐containing CPR‐type reductase. Because of the low sequence conservation inside the two classes, the conserved class‐specific positions are expected to be involved in aspects of electron transfer that are specific to the two types of reductases. In this work we present results from a conservation analysis of 16,732 CYP sequences derived from an updated version of the Cytochrome P450 Engineering Database (CYPED), using two class‐specific numbering schemes. While no position was conserved on the distal, substrate‐binding surface of the CYPs, several class‐specific residues were found on the proximal, reductase‐interacting surface; two class I‐specific residues that were negatively charged, and three class II‐specific residues that were aromatic or charged. The class‐specific conservation of glycine and proline residues in the cysteine pocket indicates that there are class‐specific differences in the flexibility of this element. Four heme‐interacting arginines were conserved differently in each class, and a class‐specific substitution of a heme‐interacting tyrosine by histidine was found, pointing to a link between heme stabilization and the reductase type. Proteins 2014; 82:491–504. © 2013 Wiley Periodicals, Inc.